Genetic Variant MCPH1:p.Val76Val (chr8-6414878-G-T) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_024596.5(MCPH1):c.228G>T(p.Val76Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 1,612,258 control chromosomes in the GnomAD database, including 498,967 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.70 ( 39458 hom., cov: 29)

Exomes 𝑓: 0.79 ( 459509 hom. )

Consequence

MCPH1
NM_024596.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:11

Conservation

PhyloP100: -1.21

Variant links:

Genes affected

MCPH1 (HGNC:6954): (microcephalin 1) This gene encodes a DNA damage response protein. The encoded protein may play a role in G2/M checkpoint arrest via maintenance of inhibitory phosphorylation of cyclin-dependent kinase 1. Mutations in this gene have been associated with primary autosomal recessive microcephaly 1 and premature chromosome condensation syndrome. Alternatively spliced transcript variants have been described. [provided by RefSeq, Feb 2010]

MCPH1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BP6

Variant 8-6414878-G-T is Benign according to our data. Variant chr8-6414878-G-T is described in ClinVar as [Benign]. Clinvar id is 158851.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr8-6414878-G-T is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=-1.21 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MCPH1	NM_024596.5 link	c.228G>T	p.Val76Val	synonymous_variant	Exon 3 of 14	ENST00000344683.10	NP_078872.3	Q8NEM0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MCPH1	ENST00000344683.10 link	c.228G>T	p.Val76Val	synonymous_variant	Exon 3 of 14	1	NM_024596.5	ENSP00000342924.5		Q8NEM0-1

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

106222

AN:

151218

Hom.:

39439

Cov.:

show subpopulations

Gnomad AFR

AF:

0.438

Gnomad AMI

AF:

0.858

Gnomad AMR

AF:

0.795

Gnomad ASJ

AF:

0.699

Gnomad EAS

AF:

0.785

Gnomad SAS

AF:

0.733

Gnomad FIN

AF:

0.891

Gnomad MID

AF:

0.661

Gnomad NFE

AF:

0.802

Gnomad OTH

AF:

0.708

GnomAD3 exomes

AF:

0.779

AC:

194367

AN:

249410

Hom.:

77206

AF XY:

0.780

AC XY:

105598

AN XY:

135306

show subpopulations

Gnomad AFR exome

AF:

0.428

Gnomad AMR exome

AF:

0.857

Gnomad ASJ exome

AF:

0.691

Gnomad EAS exome

AF:

0.787

Gnomad SAS exome

AF:

0.741

Gnomad FIN exome

AF:

0.893

Gnomad NFE exome

AF:

0.799

Gnomad OTH exome

AF:

0.786

GnomAD4 exome

AF:

0.790

AC:

1154498

AN:

1460924

Hom.:

459509

Cov.:

AF XY:

0.790

AC XY:

573782

AN XY:

726748

show subpopulations

Gnomad4 AFR exome

AF:

0.427

Gnomad4 AMR exome

AF:

0.851

Gnomad4 ASJ exome

AF:

0.688

Gnomad4 EAS exome

AF:

0.785

Gnomad4 SAS exome

AF:

0.743

Gnomad4 FIN exome

AF:

0.890

Gnomad4 NFE exome

AF:

0.802

Gnomad4 OTH exome

AF:

0.763

GnomAD4 genome

AF:

0.702

AC:

106273

AN:

151334

Hom.:

39458

Cov.:

AF XY:

0.709

AC XY:

52402

AN XY:

73858

show subpopulations

Gnomad4 AFR

AF:

0.438

Gnomad4 AMR

AF:

0.796

Gnomad4 ASJ

AF:

0.699

Gnomad4 EAS

AF:

0.786

Gnomad4 SAS

AF:

0.733

Gnomad4 FIN

AF:

0.891

Gnomad4 NFE

AF:

0.802

Gnomad4 OTH

AF:

0.710

Alfa

AF:

0.762

Hom.:

55851

Bravo

AF:

0.686

Asia WGS

AF:

0.747

AC:

2595

AN:

3478

EpiCase

AF:

0.784

EpiControl

AF:

0.784

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Genetic Services Laboratory, University of Chicago

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Aug 02, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 21, 2013

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Microcephaly 1, primary, autosomal recessive

Benign:4

Sep 05, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Jun 28, 2017

Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided

Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Mar 03, 2015

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.44

DANN

Benign

0.56

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over